Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum β-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces

Potter, Robert F.; D’Souza, Alaric W.; Wallace, Meghan A.; Shupe, Angela; Patel, Sanket; Gul, Danish; Kwon, Jennie H.; Beatty, Wandy L.; Andleeb, Saadia; Dantas, Gautam

doi:10.3389/fmicb.2018.01629

Cited by 7 publications

(8 citation statements)

References 62 publications

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“…We found 12 instances where genomes did not have >95% ANI with the identified MALDI-TOF MS hit or the most closely related genomes as determined by 16S rRNA gene sequence in the EzBioCloud database, indicating that these are putative novel genomospecies. A separate investigation found that 2/7 of the isolates unidentified by MALDI-TOF MS are a new genus of multidrug-resistant Enterobacteriaceae , termed Superficieibacter electus 31 . The previously unreported genomospecies come from the Caulobacteriacae , Xanthomonadaceae , and Enterobacteriaceae families, and five of the proposed new genomospecies are Pseudomonadaceae .…”

Section: Resultsmentioning

confidence: 99%

“…In addition to commonly recognized HAI causing bacteria, we found many potentially opportunistic pathogens and novel genomospecies from commonly pathogenic genera ( Pseudomonas , Stenotrophomonas , Brevundimonas ). The first novel genomospecies from this collection to be fully characterized, S. electus , is a new genus of Enterobacteriaceae that harbored extended spectrum β-lactamases and was multidrug resistant 31 . A previous taxonomic investigation determined that species from another novel genus of Enterobacteriaceae , Pseudocitrobacter faecalis and Pseudocitrobacter anthropi , harbored bla NDM-1 carbapenemases, and were identified in fecal samples from patients at hospitals in Pakistan 47 .…”

Section: Discussionmentioning

confidence: 99%

“…We collected surface swabs every other week for 3 months, and again at 6 months, and at 1 year, for a total of 180 samples per hospital. We identified high burdens of known MDROs on PAK-H ICU surfaces including ESKAPE pathogens and novel taxa 31,32 . This investigation is the first to show such widespread contamination with multidrug-resistant, extensively drug-resistant, and pan-drug-resistant bacteria in Pakistan.…”

Section: Introductionmentioning

confidence: 99%

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Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

D’Souza¹,

Potter²,

Wallace

et al. 2019

Nat Commun

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Bacterial pathogens that infect patients also contaminate hospital surfaces. These contaminants impact hospital infection control and epidemiology, prompting quantitative examination of their transmission dynamics. Here we investigate spatiotemporal and phylogenetic relationships of multidrug resistant (MDR) bacteria on intensive care unit surfaces from two hospitals in the United States (US) and Pakistan collected over one year. MDR bacteria isolated from 3.3% and 86.7% of US and Pakistani surfaces, respectively, include common nosocomial pathogens, rare opportunistic pathogens, and novel taxa. Common nosocomial isolates are dominated by single lineages of different clones, are phenotypically MDR, and have high resistance gene burdens. Many resistance genes (e.g., blaNDM, blaOXA carbapenamases), are shared by multiple species and flanked by mobilization elements. We identify Acinetobacter baumannii and Enterococcus faecium co-association on multiple surfaces, and demonstrate these species establish synergistic biofilms in vitro. Our results highlight substantial MDR pathogen burdens in hospital built-environments, provide evidence for spatiotemporal-dependent transmission, and demonstrate potential mechanisms for multi-species surface persistence.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

D’Souza¹,

Potter²,

Wallace

et al. 2019

Nat Commun

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“…The usefulness of WGS and phylogenomic methods in taxonomic resolution of the family Enterobacteriaceae has been previously demonstrated (Adeolu et al, 2016; Alnajar and Gupta, 2017). Recently, a novel genus was proposed based on phenotypic and phylogenomic analysis (not validated yet) (Potter et al, 2018). We determined the genome sequence of strain CCUG 66741 T in order to resolve the taxonomic identity of the strain.…”

Section: Discussionmentioning

confidence: 99%

Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant

et al. 2019

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Scandinavium goeteborgense gen. nov., sp., nov., a New Member of the Family Enterobacteriaceae 66741 T carries a novel variant of a chromosomally-encoded quinolone resistance gene (proposed qnrB96). When expressed in Escherichia coli, the qnrB96 gene conferred five-fold increase in minimum inhibitory concentration against ciprofloxacin. This study highlights the importance and the utility of whole genome sequencing for pathogen identification in clinical settings.

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“…Sample preparation, sequencing, and sequence analysis were performed as described previously (32) using 12 World Health Organization (WHO) reference genomes (18) (Table S2). Genomic DNA was obtained from pure N.…”

Section: Methodsmentioning

confidence: 99%

Genotypic and Phenotypic Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae: a Cross-Sectional Study of Isolates Recovered from Routine Urine Cultures in a High-Incidence Setting

Bailey

Potter²,

Wallace

et al. 2019

mSphere

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The objectives of this study were to perform genomic and phenotypic characterization of antimicrobial resistance in Neisseria gonorrhoeae isolates recovered from urine samples from patients in St. Louis, MO, USA. Sixty-four clinical isolates were banked over a 2-year period and subjected to antimicrobial susceptibility testing (AST) by Kirby-Bauer disk diffusion (penicillin, tetracycline, cefuroxime, and ciprofloxacin) and gradient diffusion (tetracycline, doxycycline, azithromycin, ceftriaxone, cefixime, ciprofloxacin, gemifloxacin, and delafloxacin). The medical records for the patients were evaluated to determine the demographics, location, and prescribed treatment regimen. Isolate draft genomes were assembled from Illumina shotgun sequencing data, and resistance determinants were identified by ResFinder and PointFinder. Of the 64 isolates, 97% were nonsusceptible to penicillin, with resistant isolates all containing the blaTEM-1b gene; 78 and 81% of isolates were nonsusceptible to tetracycline and doxycycline, respectively, with resistant isolates all containing the tet(M) gene. One isolate was classified as non-wild-type to azithromycin, and all isolates were susceptible to ceftriaxone; 89% of patients received this combination of drugs as first-line therapy. Six percent of isolates were resistant to ciprofloxacin, with most resistant isolates containing multiple gyrA and parC mutations. Correlation between disk and gradient diffusion AST devices was high for tetracycline and ciprofloxacin (R2 > 99% for both). The rates of N. gonorrhoeae antibiotic resistance in St. Louis are comparable to current rates reported nationally, except ciprofloxacin resistance was less common in our cohort. Strong associations between specific genetic markers and phenotypic susceptibility testing hold promise for the utility of genotype-based diagnostic assays to guide directed antibiotic therapy. IMPORTANCE Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea, which is most commonly diagnosed using a DNA-based detection method that does not require growth and isolation of N. gonorrhoeae in the laboratory. This is problematic because the rates of antibiotic resistance in N. gonorrhoeae are increasing, but without isolating the organism in the clinical laboratory, antibiotic susceptibility testing cannot be performed on strains recovered from clinical specimens. We observed an increase in the frequency of urine cultures growing N. gonorrhoeae after we implemented a total laboratory automation system for culture in our clinical laboratory. Here, we report on the rates of resistance to multiple historically used, first-line, and potential future-use antibiotics for 64 N. gonorrhoeae isolates. We found that the rates of antibiotic resistance in our isolates were comparable to national rates. Additionally, resistance to specific antibiotics correlated closely with the presence of genetic resistance genes, suggesting that DNA-based tests could also be designed to guide antibiotic therapy for treating gonorrhea.

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Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum β-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces

Cited by 7 publications

References 62 publications

Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant

Genotypic and Phenotypic Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae: a Cross-Sectional Study of Isolates Recovered from Routine Urine Cultures in a High-Incidence Setting

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